I'd like to suggest changing the feature within the Alchemy skill that randomly rewards a player with a "better" version of the item they were attempting to craft. Ex: Trying to make a Holism Elixir instead randomly produces a Holism Restorative.

While the upgrades are better, they cannot be used to make Holism Potions which provide an major instant replenishment as opposed to replenishment over time of the elixirs. If I set out to produce Holism Potions (or any Potion for that matter) and in making the elixirs I produce these upgraded version I can no longer continue making potions with them as I intended.

Best case scenario would be giving the player the option to produce the upgraded elixir or the normal one. If a player chooses to craft multiple quantities this choice dialog should not interrupt or stop the continued crafting. This way a player can still click "Craft All" for 100 elixirs and walk away from the computer, returning to see all the crafting completed and if he/she is lucky a dialog box saying "Your skill allowed you to craft 15 upgraded elixirs! How many would you like to take?" A slider and dialog box would allow a player to choose the number of upgraded batches, or zero if they choose.

Other ideas could include being able to make potions from the upgraded elixirs as well as normal elixirs.
Perhaps make the upgraded elixirs a recipe of it's own. Costing slightly more in materials.
Or alternatively, a check box that one can activate or deactivate prior to clicking "Craft" that says "Turn off random upgraded items". Something along those lines.